Mapping QC
Column
Global mapping statistics
| Total_Pairs | 234252877 | 100% |
| Total_Pairs_Mapped | 232469423 | 99.2% |
| Total_Uniq_Mapped | 220128641 | 94% |
| Total_Mito_Mapped | 498673 | 0.2% |
| Total_Dups | 98905770 | 42.2% |
| Total_Pairs_MAPQ30 | 215331878 | 91.9% |
| Total_Mito_MAPQ30 | 397362 | 0.2% |
| Total_Dups_MAPQ30 | 94300385 | 40.3% |
Column
Mapping statistics for cell barcodes
| Cell called by | FILTER |
| Estimated # of cells | 6788 |
| Fraction of MAPQ30 in cells | 65.6% |
| Median fragments per cell | 11542 |
| Library Complexity (non redudant fraction) | 55.2% |
Cell barcodes QC
Row
TSS enrichment score profile
Overlapping with sequence annotated regions
Overlapping statistics
| Fraction in peaks | 68.1% |
| Fraction in mitocondrial chromosome | 0.1% |
| Fraction in promoters | 45.5% |
| Fraction in Enhancers(ENCODE) | 23.7% |
| Fraction in TSS | 39.3% |
Row
Distribution of fragments
Total fragments VS fraction in peaks
Distribution of Insert Size
Downstream Analysis
Column
Clustering
Total reads per cell
Column
Motif Analysis
Column
Footprinting Analysis: Comparing two clusters
An example
